How can I find the selected metaball elements in Edit mode with Python?
That one's not easy. I checked the Outliner to get the path to the elements:



I haven't been able to find the full selection yet, but the active ball can be found and moved:

import bpy
bpy.data.metaballs["Mball"].elements[2].co.x += 0.1
bpy.context.active_object.data.elements.active.co.x += 0.1
bpy.data.metaballs["Mball"].elements.active.co.x += 0.1


I hope somebody can prove me wrong but it might not be exposed to the API. Metaballs don't get a lot of limelight. In which case it would be worth to find the right dev to implement it.

Only workaround I can see is to keep the metaballs separated, select them in object mode, manipulate them there(they still merge anyway) and use that selection and join them afterwards. Depends on how many you need to move.